Delimiting the genera of the Ficinia Clade (Cypereae, Cyperaceae) based on molecular phylogenetic data A. Muthama Muasya1,2 and Isabel Larridon2,3 1 Department of Biological Sciences, Bolus Herbarium, University of Cape Town, Rondebosch, Cape Town, South Africa 2 Identification and Naming, Royal Botanic Gardens Kew, Richmond, Surrey, UK 3 Department of Biology, Systematic and Evolutionary Botany Lab, Ghent University, Gent, Belgium ABSTRACT Generic delimitations in the Ficinia Clade of tribe Cypereae are revisited. In particular, we aim to establish the placement of annual species currently included in Isolepis of which the phylogenetic position is uncertain. Phylogenetic inference is based on two nuclear markers (ETS, ITS) and five plastid markers (the genes matK, ndhF, rbcL and rps16, the trnL intron and trnL-F spacer) data, analyzed using model based methods. Topologies based on nuclear and plastid data show incongruence at the backbone. Therefore, the results are presented separately. The monophyly of the smaller genera (Afroscirpoides, Dracoscirpoides, Erioscirpus, Hellmuthia, Scirpoides) is confirmed. However, Isolepis is paraphyletic as Ficinia is retrieved as one of its clades. Furthermore, Ficinia is paraphyletic if I. marginata and allies are excluded. We take a pragmatic approach based on the nuclear topology, driven by a desire to minimize taxonomic changes, to recircumscribe Ficinia to include the annual Isolepis species characterized by cartilaginous glumes and formally include all the Isolepis species inferred outside the core Isolepis clade. Consequently, the circumscription of Isolepis is narrowed to encompass only those species retrieved as part of the core Isolepis clade. Five new combinations are Submitted 20 August 2020 made (Ficinia neocapensis, Ficinia hemiuncialis, Ficinia incomtula, Ficinia leucoloma, Accepted 18 December 2020 Ficinia minuta). We present nomenclatural summary at genus level, identification Published 26 January 2021 keys and diagnostic features. Corresponding author A. Muthama Muasya, [email protected] Subjects Biodiversity, Evolutionary Studies, Plant Science fi Academic editor Keywords Taxonomy, Phylogenetics, Cyperaceae, Classi cation, Nomenclature, Cape Flora, Victoria Sosa Isolepis, Ficinia Additional Information and Declarations can be found on INTRODUCTION page 14 The paradigm shift towards recognition of genera as monophyletic entities has DOI 10.7717/peerj.10737 necessitated changes in generic circumscription (Humphreys & Linder, 2009). Within Copyright Cyperaceae, a number of changes have been made within the last decade, for example the 2021 Muasya and Larridon merger of segregate genera into the paraphyletic core in Carex L. (Global Carex Group Distributed under (GCG), 2015) and Cyperus L. (Larridon et al., 2011a, 2011b, 2013, 2014; Bauters et al., Creative Commons CC-BY 4.0 2014). A number of genera have been found to be polyphyletic, especially in the tribe Schoeneae, resolved by reclassification of entities and naming of a number of lineages as How to cite this article Muasya AM, Larridon I. 2021. Delimiting the genera of the Ficinia Clade (Cypereae, Cyperaceae) based on molecular phylogenetic data. PeerJ 9:e10737 DOI 10.7717/peerj.10737 new genera (Elliott & Muasya, 2017; Larridon et al., 2018; Larridon, Verboom & Muasya, 2018; Barrett, Wilson & Bruhl, 2019). Each of the four Cyperaceae genera recognized by Linnaeus (1753) has been reclassified over the years, with Linnaeus’ circumscription of Scirpus L. as encompassing species with bisexual flowers and spiral glume arrangement representing the most heterogenous assemblage. Embryo morphology data (Van der Veken, 1965; Goetghebeur, 1986; Semmouri et al., 2019) have unequivocally demonstrated that lineages with distinct morphology were included in Scirpus. In his seminal treatment of the family, Goetghebeur (1998) placed the 24 taxa previously named Scirpus by Linnaeus (1753) in the tribes Cypereae, Fuireneae and Scirpeae, with S. sylvaticus L. being the only species described by Linnaeus recognized as a true Scirpus and two of the species recognized as members of Isolepis R.Br. Within tribe Cypereae, the Ficinia Clade (sensu Muasya et al., 2009b) comprises taxa whose placement has been most contentious. Goetghebeur (1998) diagnosed tribe Cypereae to include species characterised by either a Cyperus or a Ficinia type embryo, where glumes are arranged distichously (Cyperus and allies) or spirally (Isolepis, Ficinia Schrad., Scirpoides Ség). Lineages bearing perianth segments were added to the clade based on molecular phylogenetic data, moving Hellmuthia Steud. from Chysitricheae (Vrijdaghs et al., 2006; Muasya et al., 2009a, 2009b), Erioscirpus Palla from Scirpeae (Yano et al., 2012), and recognizing southern African taxa previously placed in Scirpus as a distinct genus Dracoscirpoides Muasya (Muasya et al., 2012). Furthermore, the delimitation of Scirpoides has been altered to exclude Afroscirpoides García-Madr. and Muasya (García-Madrid et al., 2015) and the addition of two species that were ambiguously placed (Browning & Gordon-Gray, 2011; Reid et al., 2017). These genera are annual to perennial herbs, have basal leaves which vary in blade development, have considerable variation in inflorescence and floral morphology, and are diagnosed by a combination of morphological features (see Table 2 in García-Madrid et al., 2015). Generic delimitation between Isolepis and Ficinia is based on few morphological characters. Isolepis have a varied habit (annual to perennial) and are widespread, whereas Ficinia are perennial and predominantly occur within the Cape flora and in Africa (Goetghebeur, 1998; Muasya & Simpson, 2002). A further distinction is the presence of a gynophore in Ficinia, but several species having a gynophore and occurring outside Africa were previously excluded from the genus. For example, the New Zealand iconic sand dune taxon (Desmoschoenus spiralis (A.Rich.) Hook.f.) is embedded within core Ficinia (as Ficinia spiralis (A.Rich.) Muasya and De Lange; Muasya & De Lange, 2010), and the more widespread Ficinia nodosa (Rottb.) Goetgh., Muasya and D. A. Simpson was retained in Isolepis despite having a well developed gynophore (Muasya, Simpson & Goetghebeur, 2000). Furthermore, Isolepis may not be monophyletic as Ficinia is one of the three to four clades recovered in Isolepis (Muasya & De Lange, 2010; García-Madrid et al., 2015; Hinchliff & Roalson, 2013; Spalink et al., 2016; Semmouri et al., 2019). Challenges on distinguishing Ficinia from Isolepis have persisted over the last 200 years, as evident from at least one in six of the currently recognized Ficinia species having a validly published epithet in Isolepis (Govaerts et al., 2020). Muasya and Larridon (2021), PeerJ, DOI 10.7717/peerj.10737 2/19 We use an expanded molecular phylogenetic study to investigate the generic limits in the Ficinia Clade. We infer the phylogenetic relationships and placement of ambiguously placed Isolepis species, namely (1) I. hemiuncialis (C. B. Clarke) J. Raynal and I. incomtula Nees—which have been previously recovered as sister to the core Isolepis/ Ficinia clade; (2) I. marginata (Thunb.) A. Dietr. and allies (I. antarctica (L.) Roem. and Schult., I. capensis Muasya, I. leucoloma (Nees) C. Archer, I. minuta (Turrill) J. Raynal)—previously recovered as sister to core clade of Ficinia. The aim is to establish whether the genera in the Ficinia Clade, particularly Isolepis and Ficinia, are monophyletic, and to evaluate what characters diagnose the inferred (sub)clades. MATERIALS AND METHODS Ethics statement Part of the specimens studied were collected during field expeditions predominantly in Western Cape province of South Africa funded by grants from the National Research Foundation and with additional support from the University of Cape Town. Permit to collect these specimens were issued by the Cape Nature authorities (CN35-28-5831). The other specimens studied are available in publicly accessible herbaria (BOL, K; B. Thiers, continuously updated, http://sweetgum.nybg.org/science/ih/) and voucher details provided in Tables S1 and S2. Nomenclature and taxonomy A nomenclatural study including the taxonomic history of the genus and its species, critical for the correct coining of the new names and the proper use of prior ones, was performed. The electronic version of this article in Portable Document Format will represent a published work according to the International Code of Nomenclature for algae, fungi and plants, and hence the new names contained in the electronic version are effectively published under that Code from the electronic edition alone. In addition, new names contained in this work which have been issued with identifiers by IPNI will eventually be made available to the Global Names Index. The IPNI LSIDs can be resolved and the associated information viewed through any standard web browser by appending the LSID contained in this publication to the prefix “http://ipni.org/”. The online version of this work is archived and available from the following digital repositories: PeerJ, PubMed Central and CLOCKSS. Molecular study The Ficinia Clade, our focus group, includes the genera Afroscirpoides (one species), Dracoscripoides (three species), Erioscirpus (two species), Ficinia (81 species), Hellmuthia (one species), Isolepis (75 species) and Scirpoides (four species). A total of 166 ingroup accessions were sequenced (Table S1), representing: one species of Afroscirpoides (100%), three Dracoscripoides (100%), one Erioscirpus